Numbers made a vídeo about this once and there was a point in specific that I had tought about before too:
After the Pain Invasion Arc, there should be something like a "Civil War" Arc, with Danzo as the main villain.
Immediatly after the Invasion, with the village in shambles and Tsunade in a coma, Danzo comes in and seizes power, taking dissidents to underground Root prisoners camps and making Naruto a public enemy with false evidences against him. Meanwhile, everyone is put against everyone, with people having to choose between the self apointed "Hokage" and their friend, despite all evidence in contrary. It would be a great Arc for Sai's development for example, when he ultimatly choose tp side with Naruto instead of Danzo.
The Arc will end with a twist: When the main characters finnaly manages to prove that Danzo was behind everything and track him down, it shows that Sasuke killed him, showing his coming to the "dark side".